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Table 1 Features used in each feature set

From: The discriminant power of RNA features for pre-miRNA recognition

Feature

Reference

Feature set

  

FS1

FS2

FS3

FS4

FS5

FS6

FS7

Dinucleotide frequencies

[13]

x

      

G+C content

[13, 29]

x

x

    

x

Maximal length of the amino acid string without stop codons

[20]

      

x

Low complexity regions detected in the sequence (%)

[20, 30]

      

x

Triplets

[10]

   

x

 

x

 

Stacking triplets (X(((, X∈{A,C,G,U})

[10, 20]

      

x

Motifs (s s−substrings)

[23]

    

x

  

Minimum free energy of folding (MFE)

[27, 28]

     

x

 

Randfold (p)

[31]

     

x

 

Normalized MFE (dG)

[27]

x

x

x

   

x

MFE index 1 (M F E I1)

[29]

x

x

x

   

x

MFE index 2 (M F E I2)

[29]

x

x

x

   

x

MFE index 3 (M F E I3)

[16, 27]

x

x

    

x

MFE index 4 (M F E I4)

[16, 27]

x

x

    

x

Normalized essemble free energy (NEFE)

[16, 27]

x

x

    

x

Normalized difference (M F E−E F E) (Diff)

[16, 27]

x

x

    

x

Frequency of the MFE structure (Freq)

[16, 27]

x

      

Normalized base-pairing propensity (dP)

[29, 32]

x

 

x

    

Normalized Shannon entropy (dQ)

[29, 33]

x

x

x

   

x

Structural diversity (Diversity)

[16, 29, 33]

x

x

    

x

Normalized base-pair distance (dD)

[16, 29, 33]

x

 

x

    

Average base pairs per stem (Avg_Bp_Stem)

[16]

x

x

    

x

Average A-U pairs |A−U|/L

[16]

x

x

    

x

Average G-C pairs |G−C|/L

[16]

x

x

    

x

Average G-U pairs |G−U|/L

[16]

x

x

    

x

Content of A-U pairs per stem %(A−U)/s t e m s

[16]

x

x

    

x

Content of G-C pairs per stem %(G−C)/s t e m s

[16]

x

x

    

x

Content of G-U pairs per stem %(G−U)/s t e m s

[16]

x

x

    

x

Cumulative size of internal loops

[20]

      

x

Structure entropy (dS)

[16, 28, 29, 33]

x

x

    

x

Normalized structure entropy (d S/L)

[16, 28, 29, 33]

x

x

    

x

Structure enthalpy (dH)

[16, 28, 29, 33]

x

      

Normalized structure enthalpy (d H/L)

[16, 28, 29, 33]

x

      

Melting energy of the structure

[16, 28, 34]

x

      

Normalized melting energy of the structure

[16, 28, 34]

x

      

Topological descriptor (dF)

[29, 35]

x

x

x

   

x

Normalized variants (zG, zP and zQ)

[13, 29, 36]

x

      

Normalized variants (zD)

[13, 29, 36]

x

x

    

x

Normalized variants (zF)

[13, 29, 36]

x

      
  1. Detailed descriptions can be found in the corresponding references.
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